<!DOCTYPE html>
Family/disease information
Important note: this is a toy example and thus contains very few data points, making the algorithms less accurate
Case: classic trio-analysis
Result: sample_A is a child with a hetero-uniparental disomy at chr1
Family tree
Filter 0: single nucleotide variants
Variant statistics
Number of variants table
Allelic drop-out (ADO) & allelic drop-in (ADI)
sample_C
no two parents provided
sample_B
no two parents provided
sample_A
ADO = 15.16%
ADI = 0.22%
Variant depth
Number of variants profile
Vcf-based copy number (bam-based verification recommended)
Filter 1: filter 0, –dp.hard.limit, –af.hard.limit and –dp.soft.limit
Variant statistics
Number of variants table
Allelic drop-out (ADO) & allelic drop-in (ADI)
sample_C
no two parents provided
sample_B
no two parents provided
sample_A
ADO = 12.92%
ADI = 0.06%
Variant depth
Number of variants profile
B-allele frequency (BAF), region(s) of interest
chr1:40,707,070:100,808,080
B-allele frequency (BAF), genome-wide
sample_A (A)
Mendelian errors
Parent mapping
sample_A (A)
Filter 2: filter 0, filter 1, –keep.informative.ids and –keep.hetero.ids
Variant statistics
Number of variants table
Variant depth
Number of variants profile